Perairan Pulau Karimunjawa banyak dimanfaatkan untuk berbagai kegiatan manusia yang tentunya berpengaruh terhadap kesuburan perairan, salah satunya pada ekosistem terumbu karang yang kemudian akan berpengaruh juga pada biota karang yang ada di dalamnya. Kesuburan suatu perairan dipengaruhi oleh unsur hara (nitrat dan fosfat), klorofil-a, serta variabel fisika kimia perairan. Penelitian dilakukan pada bulan November β Desember 2014 di Pulau Karimunjawa, yang bertujuan untuk mengetahui tingkat kesuburan perairan berdasarkan kandungan NO3, PO4, dan klorofil-a di beberapa wilayah ekosistem terumbu karang Pulau Karimunjawa dan mengetahui keterkaitan antara klorofil-a dengan nitrat dan fosfat. Metode yang digunakan adalah metode deskriptif dengan teknik purposive sampling. Lokasi sampling ditentukan berdasarkan 3 stasiun dengan aktivitas pemanfaatan yang berbeda. Hasil penelitian menunjukkan bahwa kesuburan perairan berdasarkan kandungan nitrat di stasiun zona inti dan zona budidaya tergolong mesotrofik, sedangkan zona pariwisata tergolong oligotrofik. Berdasarkan kandungan fosfatnya, ketiga stasiun pengamatan tergolong dalam kategori tingkat kesuburan sangat baik sekali. Ketiga stasiun tergolong dalam kategori oligotrofik berdasarkan kandungan klorofil-a. Hubungan antara klorofil-a dengan nitrat lebih kuat daripada klorofil-a dengan fosfat yang dibuktikan pada hasil regresi linear dimana nilai (r) klorofil-a dengan nitrat sebesar 0,995 sedangkan nilai (r) klorofil-a dengan fosfat sebesar 0,143. The marine area in Karimunjawa Island is widely-used for human activities. It influences the marine fertility as well; one of them is on the coral ecosystem which also will influence the coral biota within the area. The fertility of a marine area is also affected by the hara unsure (nitrate and phosphate), chlorophyll-a, as well as the variable of marine's physics and chemist. This research was done on November-December 2014 in Karimunjawa Island, which was aimed to identify the level of fertility based on NO3, PO4, and Chlorophyll-a in the several zone on marine area of coral ecosystem in Karimunjawa Island, and to identify the relationship between Chlorophyll-a with NO3 and PO4. This research used the descriptive method using purposive sampling. The location of sampling was then identified based on 3 stations which have different application activities. The result of the study shows that the marine's fertility based on the nitrate substance in the primary zone station and conservative zone were categorized as mesotropic, while in the tourism zone was categorized as oligotropic. Based on the phosphate substance, those three stations were categorized in the extremely good fertility level. In addition, the three stations were categorized as oligotropic category based on the chlorophyll-a substance. The relationship between chlorophyll-a and nitrate was stronger than the chlorophyll-a and phosphate. It can be proven by using the result of linear regression, where the score (r) of chlorophyll-a and nitrate was as much as 0,995, whereas the score (r) of chlorophyll-a and phosphate was as much as 0,143